I have had this problem for over a year utilizing a Book, Dock, and 2 BenQ BL2420PT monitors via miniDP->DP cables from the dock. Most of the time when I boot the Book (cover closed) the screens briefly flash like they received a signal (power button goes to white) then go back to 'standby' mode a few seconds later.
I can get around this pretty simply: I have the monitors and dock plugged into a power strip. When I boot the Book, I just wait for the monitors to go back into 'standby' mode (orange power button), then simply flip the switch off on the power strip, wait about 5 seconds, and flip the power strip switch back on again. Monitors go through their BenQ splash screen and the Book / dock sync up and both monitors now work normally until the next time I shut down the Book.
I did not have this problem with my previous monitors (HP HDMI), but have had it since going to BenQ and DP. I have not tested the BenQ with the miniDP->HDMI.
Not sure if this solution will work for the rest of you, but it works every time for my situation. Before this I tried powering down the monitors then back on again, removing the power cord to the monitors and then plugging back in, removing the power for just the dock and plugging back in - nothing worked consistently until I discovered the "turn the power strip off and on again" approach.
Good luck!